Research workbench
Crystal structure of glycerol dehydrogenase (NP_348253.1) from clostridium acetobutylicum at 2.37 a resolution
Analyse Crystal structure of glycerol dehydrogenase (NP_348253.1) from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CE9
- Type
- protein
- Length
- 1,395 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol dehydrogenase
- UniProt
- Q97IL4
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glycerol dehydrogenase | protein | 349 | 57% helix, 14% strand | Q97IL4 |
| B | Glycerol dehydrogenase | protein | 348 | 56% helix, 14% strand | Q97IL4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.84 | 0.87 | 85 | ZN, EDO |
| 2 | 713 | 0.82 | 0.86 | 93 | empty |
| 3 | 368 | 0.77 | 0.87 | 57 | empty |
| 4 | 283 | 0.74 | 0.88 | 48 | empty |
| 5 | 274 | 0.68 | 0.83 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1009 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 977 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 934 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 852 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3CE9 · Crystal structure of glycerol dehydrogenase (NP_348253.1) from Clostridium acetobutylicum… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q97IL4
- Elsewhere: RCSB PDB 3CE9 · PDBe 3CE9 · UniProt Q97IL4
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